Per-base metrics on BAM/CRAM files.
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
bam
:file
Sorted BAM/CRAM file
*.{bam,cram}
index
BAI/CRAI file
*.{bai,crai}
bed
bed file containing regions of interest, where only bases from the given regions will be reported
*.{bed}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
Reference fasta (optional)
*.{fasta,fa}
fai
FAI file (optional)
*.{fai}
tsv
*.tsv.gz
TSV file
*.{tsv.gz}
versions_perbase
${task.process}
:string
The name of the process
perbase
The name of the tool
perbase --version |& sed "1!d ; s/perbase //"
:eval
The expression to obtain the version of the tool
versions
